Structure of PDB 2ybp Chain A Binding Site BS01
Receptor Information
>2ybp Chain A (length=349) Species:
9606
(Homo sapiens) [
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TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPK
SWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIP
FDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLC
SCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK
Ligand information
>2ybp Chain C (length=12) Species:
9606
(Homo sapiens) [
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PATGGVKKPHRY
Receptor-Ligand Complex Structure
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PDB
2ybp
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
Resolution
2.02 Å
Binding residue
(original residue number in PDB)
I71 N86 I87 Q88 D135 I166 I168 E169 G170 Y175 Y177 M242 S288 N290 D311 V313 K314 I315 S316
Binding residue
(residue number reindexed from 1)
I65 N80 I81 Q82 D129 I160 I162 E163 G164 Y169 Y171 M236 S282 N284 D305 V307 K308 I309 S310
Enzymatic activity
Catalytic site (original residue number in PDB)
G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1)
G164 Y171 H182 E184 H270 S282
Enzyme Commision number
1.14.11.66
: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69
: [histone H3]-trimethyl-L-lysine(36) demethylase.
External links
PDB
RCSB:2ybp
,
PDBe:2ybp
,
PDBj:2ybp
PDBsum
2ybp
PubMed
21460794
UniProt
O75164
|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)
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